Daylight Worksheet - Structural, Non-Structural, Mixture and Reaction searching with xvmerlin -- with HINTS!

xvmerlin is an XView interface to Daylight Databases which have been loaded into Merlin Pools. Day 2 will describe the administration of Merlin Pools. For today, databases have already been loaded for you. One difficulty when first trying to use xvmerlin, is proper usage of the three mouse buttons. By default the right mouse button enables you to see and select from popup menus. The left mouse button allows for selections from popup windows and to activate popup windows. The middle mouse button will display the full data tree for a given structure.

Structural Searching using xvmerlin

• Start xvmerlin and open a database:
  1. Type xvmerlin (on Sun/Linux systems) or xvmerlin4d (on SGI systems) to start merlin client . With the right mouse button select File, Open Database drag mouse to right and select medchem** database. User is "mug" password is "coffee", server is TBE.

• Superstructure Search-Finding structures in database which contain a given substructure
  1. Use right mouse button on the SMILES column and make choose the Search then Superstructures. Select Search type (try both SMILES and SMARTS), Try Grins utility to draw in a structure or type in SMILES or SMARTS. Select which type of Action, e.g. Make new hitlist. When ready hit Select

  2. Save hitlist by using the right mouse button and select the Hitlist menu from the xvmerlin window, Select Store

  Your results from your search are now stored in a hitlist which you can recall later. Select Hitlist with the left mouse button or select the menu item Set all hit to return to searching the whole database.

• Substructure Search-Finding structures embedded with given structure
  1. In the "Merlin search control panel" window change the "Look for" option to find structures embedded with given structure. Try a different Action (e.g. "remove matches from hitlist"). Make a new hitlist by combining the results with the hitlist from your Superstructure search. Select Union from the Hitlist menu. Your hitlist will now contain all structures which contain the substructure requested in the Superstructure search and those which are not embedded within the structure specified in the Substructure Search step.
  2. Try out various union/intersections of hitlists and use the left mouse button to select the SMILES column for a popup window with a larger view of the structures.

  3. Select the Display menu in the xvmerlin window and try out the Merlin keypad. Make selections with the left mouse button.

• Similarity Search-Finding structures which are similar to a given structure
  1. Perform a tanimoto similarity search using xvmerlin

  2. Perform a tversky similarity search using xvmerlin

• Non-Structural Searching
  1. Generate a similarity column in the xvmerlin window by pressing the middle mouse button just to the right of the SMILES column.
  2. Use the right most mouse button on the smilarity column to select a different datatype. Create a column containing the LogP star datatype.

  3. Find all structures which have measured LogP values between 1 and 3 and sort the results.

• Searching Reactions
  1. Open the chemsynth97demo database
  2. Search for all reactions with a reactant of your choice (e.g. 'CC(=O)OC(=O)C')

  3. Find a set of reactions that are in the same XOR cluster, is it obvious why they are grouped together?

• Combination searches
  1. Find all structures in the spresi95demo database which contain phenyl amine, have synthetic references and have a melting point <= 200.

  2. Find all structures in the wdi*** database which have both a Hydrogen bond doner and a halogen connected to an atom three bonds away and is not a trial-prep. ([O,N;!H0;R0]~[a,A]~[a,A]~[a,A]-[Cl,Br,F,I]).